Chuck versus The Intersect
by sdchuckfan
Summary: Basically picks up after the last episode of the first season. It covers the growing affection between Chuck and Sarah and Chuck's future as the intersect.
1. Chapter 1

Disclaimer: I don't own Chuck or any of the characters. I don't even own my house, yet.

Author's note: I wrote this a long time ago intended as a season finale. Enjoy.

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**_Part I: Ain't no party like a Bartowski party..._**

Chuck Bartowski has never been one for the parties that his sister Ellie threw at their Los Angeles apartment. Not that he didn't enjoy talking to people or listening to their stories, it was just that she had always used them to hook him up with any and all single women she knew. Chuck shivered at the thought of past parties where he had to actually interact with them; asking him about his plans, his job, and whether he was going to a costume party as a nerd.

But now he found himself more relaxed as he mingled around at the New Year's Eve party Ellie always threw at their home. Well, relatively relaxed since he did have to maintain his cover as Sarah Walker's boyfriend, who was actually a beautiful CIA agent sent there to protect him and the top secret information stored in his brain.

He walked through the courtyard which was full of people from the party. After a several "hellos" and "how you doings," Chuck finally made it into his home where he saw Morgan and Anna, Captain Awesome and John Casey, Sarah and Ellie all paired up talking.

"Anna, I can explain about the alarm clock. Chuck told me…"

"No, Morgan this was your choice, don't bring Chuckles into it as well."

"But sweetie, this gift came from the heart. I just…wanted to help you out with your beauty sleep. Yeah, yeah, you can never have enough beauty sleep…"

Morgan's voice trailed off as he realized the magnitude of the statement he said. Even Chuck knew the danger of those words and grimaced at the pain that was going to be inflicted by Anna.

Sometime before Chuck told Morgan about the alarm clock he gave Sarah as a Christmas present. Thinking it was a romantic gesture Morgan did the same for his girlfriend Anna, not knowing that Chuck was actually replacing one that Sarah killed with a knife at twenty paces. Besides, he gave her a proper gift of a gold necklace with a locket picked out by his sister later on.

_Saved by my guardian angel, Ellie…_

"WHAT!!" Anna shouted as she stormed out the front door.

Morgan ran after shouting "Wait honey, that's not what I meant!"

Chuck knew that nothing was ever the way Morgan meant and laughed at the scene of Morgan chasing Anna, which probably happened more often than allowed in a relationship. Chuck knew that Morgan would be ok but if he ever did that to Sarah on the other hand, he'd have to be the one running away. For his life probably.

Now John Casey was also here at the party, not only was he Chuck's co-worker at the Buymore but he was also a NSA agent also sent here to protect the intersect. Initially, Chuck thought of him as a career spy: cold-hearted, serious, all business.

But after recent events, he saw what was once a tender side to Casey after they completed a mission which involved an old love that he thought was killed by a bomb. After that Chuck realized the reason Sarah frowned upon a real relationship between working partners, the thought of losing the other was probably too great, on top of all the difficult stuff spies had to do as well.

As he walked by, Chuck couldn't help but notice the littlest of smirks on Casey's face as he talked to Captain Awesome. Shaking his head and thinking he just saw a figment of his imagination, he looked again and saw it once more.

_Hmm, who knew Casey was into life-threatening extreme sports,_ Chuck thought. But then he stopped when he realized the idiocy of his statement regarding a man who was a world-class spy and probably enjoyed taking out Afghani warloards.

"I'm telling ya Casey, nothing beats the rush of surfing in the shark infested waters of Australia. Awesome."

"Nice, Devon. But until you've jumped out of a perfectly working plane only to find out that you're main chute won't deploy and all you have left is your reserve, you haven't felt a real rush."

Devon nodded in agreement with a look of amazement and awe in his eyes. Chuck would've joined in the conversation, but his only real rush was when he was playing on his XBOX and four members of his Halo squad was killed and he had to go it alone for the rest of the mission.

Now Chuck was approaching a conversation he so desperately wanted to listen to, his sister Ellie and his "girlfriend" Sarah. As he walked closer, to his horror, he saw that Ellie had some old photo albums opened up and both of them were giggling. Even worse, it seems that Ellie had gotten a little tipsy from dipping into the eggnog one too many times.

_Nothing good can come from this._

"So out comes Chuck to receive his high school diploma, when all of the sudden he trips on his gown and falls on his face. And to top it all off, it comes flying over his head and we see this big rip open up in his pants" Ellie said right before they broke into laughter.

Chuck lowered his head in shame and tried to slink past them, only to be pulled in by a smiling and laughing Sarah.

"So hello there Mr. Underroos, we were just talking about you."

"Yeah, I could hear" Chuck smirked.

Chuck quickly turned to Ellie, "I thought you wanted me to have a girlfriend sis."

"I do, I do. But she deserves to know the real you that we all know and have grown to love."

"Well, revealing anymore of the real me will probably leave me single for life. And besides, I've graduated into the big boys' boxers now, thank you very much."

Chuck sat down next to Sarah while Ellie frantically turned the pages of the album. Both Chuck and Sarah looked on as she flipped back and forth and picked up other albums looking for something in particular.

"Wait wait I know its somewhere in here," Ellie slurred, "I want to show Sarah…the pictures of Chuck…playing with his weiner."

Instantly the blood drained from Chuck's face and he quickly jumped to his feet, adding "Dog! Weiner Dog! Dachshund actually. My other dog from when I was younger."

Chuck looked over to see a smile come from Sarah's face as she saw him panic and stumble for an explanation. "Ellie, I don't thing Sarah's interested in seeing any pictures my weiner…I mean dog."

"No, no it's fine. I'd love to see some more pictures that I can use to embarrass him with" Sarah added with a mischievous smile on her face.

Chuck just sat back down, shaking his head. _How did it turn out to this??_

"You know what, I'll let you guys get back to the Chuck historical tour and I'll freshen up Sarah's drink."

As he stood up, he heard Ellie say "You know what; I can't find that other picture I was looking for. Anyways, I wanted to ask you something. Something that I've been meaning to ask for a while now."

To emphasize the importance of her question, Ellie drew her face closer to Sarah's.

"What is it about Chuck that you love, Sarah?"

Almost immediately Chuck made a 180 degree turn and sat back down to where he was before.

"You know what? I should stay and listen in. Anyways you look quite hydrated to me. I think I'll get you that drink later."

Sarah's eyes narrowed as she shot daggers to the brown eyed man next to her. She knew he was hoping to hear some acknowledgement her feelings for him. _Couldn't he read between the lines of what happened on the rooftop when Longshore was about to haul him away?_

Suddenly Sarah was quite aware of the change in her view on life. Before this assignment, she was content to complete the mission at hand. Knowing that she did her job better than anybody else was more than enough to satisfy her. But now that old life seemed so cold and empty compared to this life with Chuck, where she was surrounded by friends.

Ellie, still waiting, snapped her fingers "Hello, anyone home?"

"Sorry Ellie, I spaced out for a second. Well, what is there not to like?" Sarah turned and ran her hands down the nape of Chuck's neck, who was clearly not complaining about the attention

Ellie, clearly looking for more, "As in? Examples please?"

_Ok I better remember next time to avoid Ellie next time she's drunk. She's more intense than many enemy interrogators. _"Well…every time I look into his face, I'm reminded of a little puppy. Cute, loving, playful, and loyal."

"Aww, that's so sweet" Ellie blushed.

Sarah continued, "But also like a puppy, he always gets into trouble and needs me to help him out of it. And he still has yet to learn the STAY command." She looked down to Chuck who clearly knew what she was driving at and now was shooting daggers back at her but after a few seconds smiled back and both shared a laugh.

They had overcome a lot in the past few months. In that short time they had their first real kiss as a bomb was about to go off, had an ex-boyfriend come back from the dead only to go back into hiding, had Sarah pushing him away for getting too close, and finally had the threat of seclusion in a bunker bring them back together again.

_Let's see any of the real relationships accomplish that,_ Chuck said to himself.

Chuck was happy to know that things as of late have gone very well between him and Sarah; they were more casual around each other without the normal tension that had built up between them. They were able to enjoy each other's company once more and finally he got back to being able to make her laugh. Pretending to be boyfriend and girlfriend didn't come so hard to each of them, although Chuck was still on the fence on whether that was a good or bad thing.

"And what about you Chuck? What is it that you like about Sarah?"

"What? Me? Well….I like how beautiful she is and how every man envies me when I'm with her. She has pretty hair, a wonderful smile, and a big beautiful pair of…." Chuck looked up, holding his hands up and saw Sarah staring him and Ellie with their mouths agape. "…blue eyes. Like the ocean."

Attempting to save himself from harm, he looked out into the distance and shouted "What's that Morgan? You need my help? I'll be right there! Sorry guys, duty calls." Luckily he slinked away before Sarah could grab his arm and let him know what she thought of his answer.

Sarah and Ellie both laughed and continued on the subject of Chuck.

"I don't think I've ever thanked you. Before he met you, he was either home in his room playing video games or out with Morgan playing video games or at work playing video games. Getting to actually talk to a real girl was just impossible. And if I ever hear about his five year plan again, I'm going to…."

"Actually Ellie, I think Chuck helped me out more than I did him. We're kinda made for each other" said Sarah. _Helped me by showing me what normal feels like and how I would miss it if it was taken away._

"But seriously, I see a big change in my brother. He has the sparkle back in his eyes, he wakes up happy to go to work, comes home with a grin on his face, and he can't wait to answer his phone in order to see if you're calling."

Sarah blushes. But then remembers the conversation before Christmas with Casey concerning her and Chuck. Casey confronted her about her relationship with Chuck and wanted to know if she compromised herself and the intersect. Sarah grimaced as she remembered what she said next about wanting to have a normal life.

But she remembered that recent events revealed that Casey did the same exact thing with Ilsa. Maybe his concern was not only for the mission of protecting the intersect but concern for something similar happening to her and Chuck. Besides, if Chuck could break her down, getting Casey to like him shouldn't be that big of a task.

Looking back to Ellie, "I guess we're both lucky to have each other. Speaking of whom, I don't see him around. I'll go look for him."

"Good idea, knowing Chuck he's probably hiding out in his room killing some sort of dwarf or ogre."

They were right of course, but this time Chuck wasn't really hiding but instead just wanted a little time alone with his thoughts.

_Interesting year_.

Sarah quietly stood at the doorway to Chuck's room and saw him sitting down with his legs propped up on his window sill. He was listening to music, drinking his beer, and just staring out the window.

Sarah quietly walked up behind him and said "Penny for your thoughts."

Chuck looked up and saw her smiling at him and replied "Sorry lady, if you didn't know my mind is now filled with scary high level government secrets which cannot be sold off to the highest bidder. No matter how beautiful the bidder is."

Sarah laughs and sits down next to his legs on the window sill facing him.

"You're in an abnormally quiet mood Chuck. Anything wrong?"

"No no, nothing's wrong. I was just thinking of how I truly enjoy seeing my sister and my girlfriend going over my more embarrassing moments with each other. Good way to bond."

Sarah couldn't resist feeling happy at the mention of being Chuck's girlfriend. Although she had hesitantly agreed to be friends, she couldn't help but flirt with him every chance she could get. A little shirt fixing here, a little hair combing there and it almost seemed like they were in a real relationship. And don't mention the joy she felt whenever Chuck walked into the Wienerlicious for lunch, which he now started to do everyday he worked.

"And what ever she said happened with me and the jello in eleventh grade is totally …. Wait, she didn't tell you about that did she?"

Sarah shook her head.

"Uh ok, forget I said that and let's move on."

Sarah, now curious, decidedly moves on and asks "so really Chuck, shouldn't you be out and about mingling with everyone?"

"I should but I couldn't help but think about what's happened this year. All of these missions where people's lives hang in the balance, I can't help but think I might be in over my head at times."

"For someone who says they'd run away from a fight, you tend to do a lot of running towards the action" Sarah included. "Which part of STAY IN THE CAR has you the most confused?" she said laughingly.

"I know, I know. My mind says STAY WHERE ITS SAFE, but my gut tells me to GO IN AND HELP. Luckily I have you and Casey to guide me and save me. Speaking of which, I'd like to thank you again for all the times you risked you're life for me."

"I think we're even so far, you've saved me in more ways than one" Sarah replied thinking not of the physical events, but of how he saved her from being just another career spy.

"Well then, I guess it hasn't been that bad of year. Besides who would've thought that I would have also landed a great girlfriend…only it's too bad that this relationship is just a cover."

Sarah paused for a second. "Well Chuck, I'll let you in on a spy secret. No one, I mean no one, can live in a cover this long as I have without something real about the person coming out. The only way to make a believable cover is to be yourself, that way there are less lies to remember."

Chuck is clearly intrigued by this and asks her "so which part is the real part, Sarah?"

"That's for me to know…" Sarah says smiling.

"And for you to torture me should I ever find out right?" jokingly Chuck adds. "But truth be told, I think I know more about you than you realize."

"Oh really, like what?"

Chuck pointed into the ceiling, indicating that he didn't want to say anything into the bugs that Casey placed in the room.

"Don't worry Chuck, Casey told me he turned them off tonight. All the noise from the party will interfere with them anyways. So go ahead and impress me with your detective skills."

"You don't sound too confident in my skills Agent Walker. I guess I'll have to change that for you. Let's see, first I know that you don't like olives."

Sarah grinned, "oh, you got me there. It wasn't like I was picking the olives off in front of your face."

Undeterred, Chuck went on. "I also know that you cry at sappy romantic movies. You try to hold back the tears, but I saw your eyes watering."

"It was a touching movie ok?"

"It was the movie Stardust."

"Yeah and so? It was so sad when she woke up and thought the love of her life left her behind."

"It was Stardust. Stardust, the movie with Deniro as a gay pirate."

"Ok fine. I liked the movie anyways. Besides, I don't get to watch movies that much."

"Hmm, let's move on. Three, despite the fact that you try to portray yourself as the big, bad CIA agent, you still are a girly-girl who likes to dress up and put on make up. Which, now that I think about it, kind of fits in." Chuck smiled, showing his contentment in the observations he made.

"Are you complaining? Last time I noticed, your jaw was on the floor when I walked in this evening."

Sarah now leaned in closer to Chuck and teased, "Is that it detective? And here I thought you were going to impress me with your observation skills. Tsk tsk, nice try though."

Chuck now leaned in closer as well, "I didn't say I was done did I? Those were the easy ones. I just wanted to give you a way out before I started on the hard stuff."

Now Sarah was starting to worry. _What does he know about me?_

"I know that look. Don't worry Sarah, I don't know the exact details of your life but I do know what's going on up that noggin of yours. You ready?"

Sarah nodded and indicated for him to continue.

"Here we go." Chuck paused for effect and then continued, "I know that your desperately yearning for the real life, with me." Sarah was taken aback, knowing that it was the truth but kept her game face on to not give anything away to Chuck.

"I know that you lived an exciting, adventurous life globe trotting and saving people, but after a while it gets old, right? Now I think after all that you've done, the only thing you have left to accomplish is to live in the real world. I don't know why, but I get the feeling that you don't think you deserve to live out with the rest of us. Let me tell you now, no one deserves it more than you."

Sarah was still not giving any indications acknowledging or denying what he said. But deep inside she knew this was true. She longed to live with Chuck and enjoy time with the friends she made. Chuck was wrong about deserving it though, _he doesn't know the things I've done, the people I've hurt._

"Don't worry about saying anything. I'm just tossing my thoughts into the wind. Should I continue?"

"Of course Chuck, I'm interested in hearing your deep insights."

Chuck now leaned in, bringing his face within inches of Sarah's. She couldn't help but blush now that his deep, brown eyes were staring right at her.

"I know that you're afraid of me."

Sarah's eyes popped wide open before she started to laugh. "Afraid? Of you? You know how many ways that I can kill a person?"

"Yeah yeah, I've heard that you know how to kill a man between 50 to 100 ways. The number varies. But still, you're afraid of me."

"Ok smart guy. Why am I afraid of you?"

"Easy, first I represent the real world and the agent inside of you is afraid of my influence. Agent Walker is afraid that I might be getting through to Sarah Walker and drive her into the real world. In spy world you're in the top of the food chain. No one else probably can match your skills. But in the real world, compared to you, I'm the top dog and that scares you."

Sarah was now getting uncomfortable. _Was I that transparent? I was always careful to hide my emotions and to keep up the barrier I had placed to keep people out. How is it that Chuck can see right through the façade and see the truth?_

"Second, in order to assimilate into the real world, you'll need someone to help out. But in order to do that, you'll have to do something totally out of character and something that will rock you world. You'll have to trust someone."

Chuck stood up and sat down on the window sill next to Sarah. "You once asked me to trust you and I did. I trust that you will keep me safe in spy world. Now I ask you the same thing. Trust me. Trust me to keep you safe in the real world."

No one asked her that before, Sarah was stunned. A single tear ran down her face as she hasn't been this touched before. Chuck was more observant than she thought and despite his lack of physical strength, he made up for it with his emotional strength. _What should I say? What should I do? He's left himself out there for me to either embrace or crush._

Noticing that Sarah was wriggling around, looking uncomfortable on the windowsill, Chuck offered "Don't fret you pretty little head about confirming anything or answering anything. Let's just call this an exercise in observation and insight. I doubt that I was close to the truth though."

Almost to the point of being inaudible, Sarah whispered "closer to the truth than you think, Chuck." Sarah looked up with her moist eyes and smiled at him.

As they share a long, warm look into each other's eyes, they hear everyone counting down from thirty, signaling the coming of the New Year.

They both stood up and Chuck stated "well I guess for the sake of our cover, we should do what couples normally do when the clock strikes twelve. Don't you think?"

"For the sake of our cover then, I'll be forced to kiss you."

Chuck laughed, remembering a similar conversation in the past with Sarah.

"Forced? Would it be so bad?"

"I guess I could suffer through it" Sarah quickly replied.

As the count reaches one, Chuck drew Sarah closer until their lips were almost brushing each other. _Finally a kiss without a bomb threatening our lives_, Chuck thought. That is until Morgan made his ill timed entrance into his room.

"Whoa, whoa, whoa, get a room you guys!"

Pulling away from the almost kiss; Chuck shouted "we did, until you came in!"

Sarah quickly walked away from Chuck and Morgan, who were arguing about his sudden entrance into his room and ruining the mood.

Although she did enjoy the tender moment with Chuck, still something inside of her held back all of which she wanted to say; about how she cares for him, how it was him she chose over Bryce and how she desperately wanted to have a normal life with him.

Once again her CIA training took hold a prevented the release of such vital information which could have compromised her. She kicked herself for once more missing the chance and could only hold back the tears that were forming.

Casey, now outside in the courtyard, received a call from Beckman on his cellphone.

"Hello, general. What can I do for you?" Casey asked, knowing full well what orders lay ahead for him.

"Casey, the time has come to take care of Bartowski. The beta intersect is up and running and all liabilities from the previous incarnation are to be terminated. Understood?"

"Yes, ma'am" he replied with a hint of anger in his voice. He slammed his phone shut.

He dreaded the time when the order to eliminate Chuck would come. Although he tried to distance himself from the subject, he couldn't help but grow attached to him.

Throughout their time together, Casey grew to feel that Chuck had handled himself admirably. In difficult life threatening situations, he has shown himself to be a quick problem solver and an extremely loyal partner, something that was missing nowadays in the spy world. The worse part was that he didn't sign up for that kind of life and took no oath to lay down his life for his country. Yet Chuck took it all in stride when others would've crumbled.

And although Chuck and Sarah had grown closer than he would've liked, they never let it interfere with the mission at hand and it actually made their determination to complete missions in order to hide it even that much stronger.

Casey walked back into the Bartowski home and said goodbye to everyone. He eventually made it to Sarah and Chuck, who were now sitting in the living room.

Chuck, sensing something, said "leaving so soon buddy? The party's only started."

Looking to Sarah, Casey replied "I have some things to CLEAN up at home, you know WORK related things. Can't have them piling up in the New Year."

Casey hoped that she would read between the lines and get Chuck as far away as possible. But Sarah still looked unaffected as he walked back into his apartment.


	2. Chapter 2

The next few days after New Year's were quite uneventful for Chuck and his team. They were given some time off by both Beckman and Graham but considering bad guys usually don't take holidays, Chuck was on alert for any flashes.

One thing bothered him though; Casey was gone for two days without notice. This was unusual considering the level of seriousness Casey placed into any job, even one selling appliances.

He quickly found Morgan, who was in the middle of talking to Lester and Jeff about how he won Anna back after their New Year's fight.

"I'm telling you guys, all I did was stand my ground and tell her it was all a big mistake. No fuss, no muss. I let her know who wears the pants in this relationship."

Lester and Jeff clearly looked impressed until Chuck added "Yeah and you clearly said it was Anna. Actually more like scream it….like a little girl after she put you in some weird choke hold."

"Dude, you were supposed to keep that between us amigos" Morgan implored.

"I think it's hard to keep it between us when the whole block heard you call her 'Big Mama'. Now, where's Casey?"

Now dejected, Morgan answered "no idea, he gave his resignation yesterday and took off. No explanations or anything."

"What? And you didn't tell me?"

"Sorry dude" was all Morgan came up with as Chuck walked out the store heading for Wienerlicious.

As he walked into an empty store to see Sarah in her German/Swedish/Bavarian something or another get up for work, he couldn't help but smile at the fact that she was a super spy cooking gourmet wiener dogs.

"Hey Chuck, your usual order for lunch? Weiner?" Sarah asked clearly still prodding him about the embarrassing scene at the party.

"No, not…have you seen or heard anything from Casey lately?"

"Not since the party. Why? What's wrong?"

"Its just that yesterday he quit from the Buymore without giving any explanations. I know he wasn't the emotional type, but I expected at least a goodbye grunt or two."

Now the gears started moving in Sarah's mind and she then realized the clue she missed; Casey was trying to give her a head start when he said he had to "clean up" at home. Sarah cussed at herself for missing the hint and even more at the fact she lost valuable time needed to hide Chuck away.

Several months prior, she would've thought nothing about eliminating the target. It was her job of course and CIA training taught her that sometimes the need of the many outweighs the need of the few, or one. Eliminating one target in order to protect thousands more seemed like an easy decision to make.

But this time, it wasn't that easy. Chuck willingly risked his single life in order to save the lives of many and he did this not because he forced to, but because he wanted to. He willingly gave his life to the cause, lied to his friends and family, and placed himself in harm's way in more than one occasion.

More than anything, Chuck introduced her to something she had been missing: family, friends, real love, and a normal life. Sarah normally pushed her feelings aside in order to make it easier to complete the mission at hand, not this time. No, this time completing the clean up mission was going to be difficult and she was going to make it so for anyone who got in their way. Casey included.

Sarah quickly went into action mode, grabbing Chuck and heading out towards her car. The only thing she could do now is head back to her place and grab all the supplies she would need to get him into hiding.

Chuck, slow in grasping the situation, asked "What, what are you doing Sarah? Where are we going?"

"Chuck, I think Casey received orders to eliminate the intersect. Eliminate you."

"Wha, Wha…why would they do that? I'm fully cooperating with you guys and clearly I'm too much of a chicken to do anything with the data."

"That's not it. They must've had sort of back up in place just in case the first intersect was destroyed. They're trying to clean up their mistakes and pretend this all didn't happen. What we need to do now is get to my place so I can get all the things we need to make you disappear for a while."

Now Chuck fully realized the enormity of the situation and his only hope was a CIA agent in a Wienerlicious outfit. _I'm doomed…or in Quentin Tarentino movie._

"Trust me Chuck. I won't let anything bad happen to you."

"I do Sarah." As he said this, even he knew that this might be too much of a task for even her to pull off. Sarah was a great agent, but pitting her against a whole agency might be too much to ask.

They quickly left her place after getting all they need to fend off any attempts at Chuck's life. He was still in awe in how many weapons can be hidden in a small hotel room while they headed out in Sarah's Porsche. But as soon as they leave the garage, Sarah noticed a blacked out Ford Expedition following them around 30 yards away.

"Darn it, the NSA is already on us."

Chuck looked back, "Wow, and I thought that 30 yards was just an approximate distance for tailing. They sure follow protocol."

"Yeah and that protocol is why were in the mess we are today, Chuck."

Sarah repeatedly tried to shake them off their heels, but to no avail. The SUV sped up beside them and rammed into the corner of their car, causing them to spin out violently and crash into a telephone pole.

With both Sarah and Chuck groggy from their rollercoaster ride, the NSA agents would have no trouble in apprehending them and fulfilling their mission orders. They quickly turned their truck around and came in close to the smoking Porsche containing their target.

Just as they started opening their doors, another Expedition slams into their side, causing all the occupants to be thrown onto the other side and knocking them out.

Sarah, witnessing the events, quickly freed herself and proceeded to slap an unconscious Chuck.

"Chuck, Chuck, Chuck, wake up already."

"What? Ouch, quit that. Are you trying to complete their mission for them?"

As they extricated themselves from the wreckage, a familiar voice rang out to them.

"Agent Walker, Bartowski, get over here. Now."

Shouting out of the SUV window was Casey, who they realized had just taken out his fellow NSA agents. Casey was a career spy, loyal to the agency and even more loyal to his country. But still here he was, rescuing Chuck and Sarah from orders that he himself also received.

"Casey, what are you doing here? And more importantly, why should we trust you?" Sarah asked.

"I would think that a little gratitude for risking my life, abandoning my career, and missing a new episode of Law and Order would be the proper response, Walker."

"You didn't answer my quest…."

"Do you really want to do this when more guns will be arriving than even I care to see?"

"Gotta agree with Casey on this one. Sarah, get in the car."

Before the unconscious NSA agents could wake up, they were speeding off to an unknown destination. Things remained quiet in the car, until Chuck spoke up and asked the most obvious question for their current situation.

"Aren't you supposed to be trying to kill me, Casey? Not that I'm not grateful to be alive and not full of bullet holes, but you did receive orders to eliminate me."

"Yes I did and now I'm disobeying them. That's all that needs to be said; if you want more out of me, I can pull over right now and let them discuss it with you."

"Well that's all I need to hear, what's the plan?"

Sensing Casey's inability to answer Chuck's question, Sarah asked "you do have a plan right? Please don't tell me that all you came up with so far is ramming the agents with your truck."

"Well….I've had a difficult day ok? Besides, this disobeying orders thing is new to me. Maybe you should take the lead Walker, disobeying orders might come easier to you."

"Funny. Doesn't help us much in the current situation though."

Sarah knew that the NSA was slowly closing in on them and without any planned course of action, they'd be caught for sure. She quickly tried to run down their options: try to hide and be forced to live a cover for the rest of their lives; or take out the new intersect so that Chuck would once again be important to the cause.

She grimaced at the thought of either of these scenarios playing out; although as a spy she would be able to quickly slip into a new identity, Chuck on the other hand was a civilian and not used to shedding one. Besides, she would be taking him away from the things that attracted her to him in the first place, family and friends.

That left one viable option: take out the new intersect and establish Chuck's importance once again. Sarah knew this would only be a short fix; in six months another intersect will be built and the clean up order will go out again. But running out of choices, this was the one that could buy them more time.

Turning to the driver's seat, Sarah tells Casey "there's only one choice we can make here."

"I know, take out the beta intersect. I just realized the same thing; although we'll back to this same position in the future."

"We can't worry about that now; Chuck's safety is first and foremost. We'll deal with that when the time comes."

Sitting quietly in the rear seat, Chuck's mind was now grasping the risks Sarah and Casey took in protecting him. They were willingly sacrificing everything for him and he couldn't help but feel a little undeserving of the devotion.

Casey told him once before that they couldn't save one person if it meant that millions more would be in danger. Now Casey was contradicting what he said; now he and Sarah were in danger trying to rescue him. This did not sit well with Chuck at all.

"We need to head to the Buymore, Casey. It's the only place we can access the info on where the new system is located. Its probably gonna be a big risk; they might know we're coming" Sarah said.

"Oh well, I always wanted to end it in a blaze of glory."

They pulled up in the Buymore parking lot, scanning the area for any clues to a trap. After a few moments of looking around, Casey and Sarah nodded at each other, signaling that everything seemed fine for the moment.

Casey was the first to speak. "Ok, here's what we're gonna do. Sarah and I will run into the store and access all the data we need to destroy the beta intersect. We'll quickly exit the store, hopefully injuring some people who get in our way. Chuck, you…"

"Yeah, yeah, yeah. Stay in the car. Have you guys ever thought that the bad guys would look in the car first sometimes?"

Casey gave one of his grunts, which Chuck interpreted as one of the ones that signal his approval. Sarah, on the other hand, could only smile at how Chuck still remained fairly calm despite his safety being in their hands. She knew he trusted her with his life and that fact strengthened her resolve.

Sarah and Casey entered the Buymore from the back entrance and quickly scanned the room. As they walked near to the home theater room, the doors swing open and thirty NSA agents quickly surround them before they could even get a shot off.

"So much for blaze of glory."

Chuck was listening in from the microphone in Sarah's watch and a look of dread fell on his face. What he feared the most had happened: in trying to protect him, his friends will end up getting hurt.

Back in the Buymore, Sarah and Casey were disarmed and handcuffed when they see NSA General Beckman and CIA director Graham walk out. Sarah and Casey were surprised to see the higher ups actually get out into the field but they knew the importance of the intersect to everyone.

"Very disappointed in you, Casey. You're the last person I thought would disobey orders" Beckman said.

"Yeah, new concept to me too. Not very disappointed thought."

Graham turned to Sarah, "And you as well Sarah, you let your emotions once again cloud your judgment. Did you really think you guys had a chance of hiding the intersect?"

"This time, my emotions were telling me the right thing to do. I won't sit back and do nothing as an innocent man is killed."

"Very noble of you both and I understand the loyalty to Bartowski, but in this situation, the greater good must prevail. What he knows can hurt a lot of people should it fall into the wrong hands. And now that we have the beta intersect, we need to eliminate that risk."

Just as he finished he sentence, two agents walk in with Chuck in tow.

Turning to Casey and Sarah, "what did I say about the car?"

"Very well, we're sorry we have to do this Bartowski. But the information you know is…"

Chuck cut her off, "…too dangerous to have walking around L.A., I know. What happens to agents Casey and Walker now?

"Well they both disobeyed orders and went against their agencies. There are severe punishments for those who betray their government."

"They were just trying to protect me."

"Even though they were doing what was right, sometimes the right of the many outweighs the individual. They knew this would happen if they were caught."

"Look, I've done all the things you guys asked of me without asking for anything in return. Now I'm asking, please forget what they did here today and just discharge them or something."

"Fine, we'll consider it. As for the matter of you…"

Before she could finish her sentence, a call comes into her cellphone. Looking at the caller id, a look of surprise washes over the face of Beckman.

"What is it? What? How could that happen? Yes, we're on our way now. Evacuate everyone from the level and institute a lockdown of the building."

Graham, looking surprised as well, "what is it?"

"The beta intersect. It has independently instituted the fueling of all ICBMs in the United States. We need to head to the compound now. Bring Casey, Sarah, and the intersect as well, we might need their help."


	3. Chapter 3

Part III: Intersect meet intersect

* * *

Everyone was escorted into the beta intersect facility located conveniently within Los Angeles. Time was a commodity they didn't have plenty of; once launched, those ICBMs would reach their target within the hour. The millions that would be in danger erased all thoughts on the previous mission to eliminate Chuck; they might end up needing him after all.

What Chuck had failed to tell the others at the time was that he had flashed as soon as Beckman said the words "beta intersect."

Amid the random pictures cycling through his head were the initial schematics and diagrams. Four supercomputers, each one composed of 4000 smaller computers that were highly interconnected by high-speed network. This legion of cpus provided the muscle for a sophisticated neural network designed to detect novel patterns and sequences and make sequential decision making. _I guess I know what decisions it's making_.

He also found that both intersects were planned out at the same time; one just got finished earlier and thus had the data on the other. _Lucky break._

On the outside it looked like any other abandoned warehouse, although warehouses usually didn't have a secret elevator going deep underground. Chuck counted the number of floors listed on the elevators computer screen and was amazed that they could hide a facility so huge in the middle of L.A. _I'd hate to see the power bills for a place like this._

As the doors opened up, lights were flashing and sirens were blaring; Beckman shouted "let's go. The beta intersect is located down the corridor to the right."

Sarah, obviously confused about the situation, asked "General, but how could the intersect order the fueling of those missiles? If it's just like the previous incarnation, then all it should do is show data correlations."

"This is not the same as the previous one. In seeing how Bartowski was better at determining connections, we decided to upgrade the beta with an AI, artificial intelligence. We were hoping it would be better able to mimic human intelligence."

Casey added "but that would not explain our current situation, General."

"True. We also gave the computer the ability to make quick decisions when it saw a specific series of events coming together which could jeopardize national security."

"What? You gave the computer that much control?" Sarah said.

"We thought at the time that the beta unit would be more reliable and a quicker responder than any person could be."

Sarah was starting to get angry, "true, but what of the parts of human mind that you can't copy and that are just as important. Where is the compassion, loyalty, and respect for other people?"

Before the general could answer, they arrived in the control room next to the intersect. What Chuck saw was a bank of large monitors showing correlations of data from both the NSA and CIA, basically what the beta intersect was thinking. Then to the other end of the room was a glass wall separating them from the main beta intersect unit, with a smaller clean room used to enter into it.

Once again, Chuck flashed as soon as he saw the glass walls. Everything this time came into his mind: the designs, the programming, the access codes, and the security system that was in place.

Sarah saw the look on Chuck's face and immediately knew he had flashed on the intel for the new intersect. "Chuck, what did you see?"

"Bill Gates' nightmare."

Casey was already sitting on one of the computers which were used to monitor the intersect and give directions should the need arise. "Sarah, take the other seat. We have fifteen minutes to figure this out."

Sarah nodded and sat down next to him; Beckman and Graham stood over them and looked at the bank of screens. It was as they feared; the beta intersect was launching the ICBMs because it mistook an unscheduled Chinese military naval practice as an actual attack on the United States.

"Casey, tell the beta unit that it was just military maneuvers. Tell it to stand down" Beckman ordered.

"I would, but according to this the unit has cut off all connections to the outside. It has shut itself off from human contact in case the people running it were compromised."

Sarah asked "so there's no way to talk to the unit and shut it down?"

"No, not unless we do it from the main unit itself."

Beckman spoke up "and to gain access while the unit is locked down like this would need someone who knows the passwords to the firewalls."

Chuck's eyes lit up, "I know them. I saw some of them when I flashed earlier. I'll just go in the room and type it in."

Chuck turned around and looked into the glass room, "the only problem is that smoke in the room; it'll make it hard to see the screen. And those sleeping people on the floor…."

Graham spoke up, "Chuck that's not fog, that's a derivative of agent 15. Agent 15 is normally non-lethal incapacitating…"

Chuck had flashed on the reference and finished the sentence, "chemical which initial effects include blurred vision, increased heart rate, difficulty thinking, disorientation….which usually takes effect around 30 minutes to 4 hours."

"Correct. But this derivative was adapted to work within a minute or two and can be absorbed through the skin. In the event of longer exposure, it will also kill."

"Great, that's nice to hear. I'm glad to see good taxpayer money going into making stuff that's non-lethal into lethal ones. Not that there's not enough stuff out in the world to kill us," Chuck said with a smirk. "Can't you get me a containment suit or something?"

"Can't, the gas has been changed to work through all know filters as well. After the Bryce incident, we didn't want to leave anything to chance."

"Of course. Don't want to make it easy or anything."

As Chuck looked around he saw the map marking the targets on Chinese soil and the possible retaliation sites in the U.S. by the Chinese. These were major cities; millions and millions of people inhabit these areas and now might be killed unless the beta intersect was shut down.

Chuck then looked into the room and a dread came over his face. Normally he would've left this heroic stuff to the agents assigned to him, but this time no one could do anything but him. _The decision shouldn't be this difficult_. _My life for the lives of millions seems like a fair bargain._

He then turned to see Casey still typing away on the computer; frantically trying to re-establish the connection with the beta unit.

Sarah looked up just in time to see the look on Chuck's face that she feared. She could see that he had made a decision on what to do. The CIA part of her said that it was the logical choice to be made and that his life needed to be sacrificed. The civilian side of her didn't want to see Chuck gone from her life; he taught her that every life was important.

Seeing the determination on his face, Sarah shouted to him "Chuck, I know what you're thinking. But I…we can't have you sacrificing yourself; you're way too valuable. Give us time to try to link up again with the beta unit."

"Don't worry Sarah, that's not what I was thinking. I was thinking that all programmers leave a back door to their programs in order to quickly access the vital systems in times of emergencies."

"Good thinking Chuck. I'll see if I can access any of the non-vital systems…"

But Chuck knew there were no such entrances. He flashed on the programming and it was as secure as a program could get. _How I wish for an Irene Demova virus._

As Sarah turned around to look back at Chuck, she found that he wasn't there and what she feared had happened. She quickly scanned the room hoping to find him in a corner or something, but not this time. She hesitantly lifted her eyes and looked into the clean room attached to the room of the beta unit. There, to her dismay, was Chuck locking the door.

As she ran down to the room, Casey and the others looked up to see the same sight. Sarah made her way down and started shouting, "get out of there right now Chuck! What are you doing?"

Speaking through the room to room intercom, Chuck said, "Sorry Sarah, no other solutions. Remember, intersect-guy here. I kind of know all there is to know."

"Get out here right now or I'll…I'll…I'll shoot you were you stand!" Sarah said as she un-holstered the gun from her back.

Graham seeing what was happening shouted to Sarah, "Walker, if you shoot the glass, all the gas will leak into this level. We all will get a lethal dose."

Chuck, still looking at Sarah, smirked "You know you really need to work on this instinct of yours. You're going to shoot me to prevent me from being killed by gas?"

Sarah threw the gun down and pleaded "Chuck, there's got to be another way…"

"Nope, there's not. If there was I wouldn't be here, right? Besides, I've made my decision; I want to be a hero" referring back to a conversation he had with Sarah about some wanting to be a hero and other needing to be asked.

Seeing that Sarah wasn't moving away, Chuck said "it's ok, I'm surer of myself now than I was anytime before. I 'm making the right call."

As Sarah slowly walked back to her seat, Chuck now looked up to Beckman, "General, I'm betting now you're glad that Casey decided to disobey orders."

Beckman couldn't say anything but the shame on her face told plenty.

"Graham, Beckman. One more thing. No retaliation." Both of them turned and looked at Chuck.

"No retaliation against Sarah or Casey for the incident earlier."

After looking at one another and nodding in agreement, Graham asked "what earlier incident Bartowski?"

Sarah looked up at Chuck in amazement; e_ven now of all times, he still thinks of others over himself. Once again he's saving me and still I can't even tell him what I really want to say._

Casey, now obviously touched by the gesture, "Chuck, thanks. I'm sorry if I didn't say this before, but you're a good man. You have my respect."

"Thanks Casey."

Now turning back to Sarah, who looked more panicked than before, Chuck asked "Sarah, I know I'm asking a lot again but would you mind taking care of Ellie, Morgan, Awesome…everyone I knew? Tell them I died during something cool, like during sex or a 72 hour Call of Duty marathon."

Sarah, smiling a bit, said "don't say that, you'll be fine."

As she said that, Chuck opened the door into the beta unit and walked into the gas. He didn't look affected and quickly walked to the corner of the room.

_Computer intersect, meet the human intersect._

"Ok, probably should've asked this before but how do I input the commands again? I don't see a computer terminal anywhere."

One of the techs stood up, "There is no keyboard or mouse. It is all done through those VR glasses and gloves you see sitting there. Once you put them on, you'll see what you need to do."

Chuck quickly stepped into the center of the room and put on the equipment. Once on he saw 3-D virtual monitor and a virtual keyboard near his hands. As he moved his head around so did his view in the virtual world and the same thing with his hands; as he moved them so did the virtual representations. _So cool. Would've loved to have used this on that SOCOM tournament._

"No sweat. Starting to take down the firewalls. How much time do I have and how many passwords?"

"You have roughly 10 minutes Chuck and there are 20 firewalls that need passwords" Sarah replied.

"30 seconds for each firewall? You guys aren't making this any easier on me. So much for trying to get out of here before I start loosing bowel control."

Five minutes later, Chuck had passed through the first ten firewalls as calculated. Sarah couldn't believe the speed that his hands were typing into the virtual keyboard. Even the techs were remarking that he was progressing faster than they ever could, even with the gas. Her awe of Chuck was short lived as she realized that this might be the last thing he would be doing. _Last thing._

Even though Chuck had started at the anticipated rate, the toll the gas was taking him was evident to everyone in the room. What everyone didn't know was that the gas affected him instantly. He suddenly felt his heart race as if he had just completed a 100 yard sprint and he found it hard to focus on a single thought.

He had started out standing, but now was now sitting on his knees with his shoulders slumped over and his hands barely above the floor. His head was also slumped forward onto his chest. The only way they knew he was still alive was that his fingers were still moving, typing away at the keyboard.

One of the techs whispered to the other that he had slowed down considerably and that he was taking more than 45 seconds for each firewall which would mean that he wouldn't make it in time.

Overhearing this, Casey set up a secure line to Chuck. Giving her the microphone, he quickly said "one on one with Chuck."

Sarah sheepishly took the mic; she had no idea what to say or what to tell him. "Hey Chuck, Sarah here. How are you feeling? You're doing great in there…"

As soon as that last word came out, Casey cut the line and shouted to Sarah, "what the hell was that? How are you feeling? He just sucked in major amounts of poison, how do you think he feels?"

Sarah, taken aback, replied "what do you mean, what do you want me to say?"

Now Casey was feeling anger well up inside of him. "Listen Walker, what do you think he's gone in there for?"

"He's giving his life to stop those nukes before they kill innocent people, that's what's he's doing."

"Correct. Giving his life up. Now listen, I've been in this game longer than you and let me tell you something. I've seen many men come in and say that they would give up their life for their country and you know what? They usually do one way or another and I had no problem with it. You know why? Because they decided to take an oath to uphold their ideals, to protect something bigger than themselves; Chuck did not. He had no choice and was instantly plunged into this happy world of ours. Now I'll be damned if he gives up his life because some idiot made a stupid decision and he has to clean it up."

Sarah couldn't help but shrink back from the Casey's assault. "What should I do?"

"What you should do? I'll tell you what you should do: give him hope. Tell him what he wants to know, what he needs to know in order to survive and endure the pain he's in. And if your stubborn CIA head won't let you say what I obviously know what you want to say to him, then lie. Lie through your teeth and make him believe it. Just make it so that he doesn't give up and think that he has to go down with the ship."

Sarah could see the conviction in Casey's eyes and she knew that he had been compromised as well. She slowly nodded to him and put the mic back on as she walked into the corner of the room.

"Chuck. I need to tell you something. Don't worry, its just me and you listening and it's ok if you don't respond. I just need to say what I should've said a long time ago to you, what you've wanted to hear. Since I've met you, something strange and scary has happened to me. I've let you, my asset, get closer to me than anyone in my life before has gotten. And all you've done is just be yourself and included me into your life."

Still Sarah didn't see any difference in Chuck as he slowly plugged away at the firewalls.

"What I'm trying to say is that you've started a change in me and it scares me. You have me questioning my duty and obligations to the agency. I went from living for the next rush of a dangerous mission to living for the quiet moments at home. I've found myself wanting a real life with you. Now you can't start this change in me and then leave it half finished. I want you to complete what you started."

Now with a sterner voice "So, I need you Chuck to promise me that you'll come out of there alive. I want you to do whatever you can to work faster and get out of there so that we can treat you. I want you to live and come back to us. To me."

After a few moments of silence Sarah heard on the headset, "You…have…such bad timing. And has anyone told you that….you're kind of demanding."

Smiling, "I know Chuck; you bring out the worst in me."

"And …you in me."

Suddenly Sarah notices Chuck's hands typing faster than before and then looks up into the control room.

"Amazing! He's sped up. He's now passed through eight of the ten firewalls. Less than a minute remaining till nuclear launch" shouted a nearby tech.

"Ninth wall down. Twenty seconds remaining."

"Excellent! Tenth wall down. Starting beta intersect shut down."

Everyone looked up to the map as red dots indicating imminent launches suddenly turned green showing that they were powering down. Loud cheers filled the room as everyone was able to let out the breaths they were holding for the last ten minutes.

"Chuck!" Sarah shouted as she saw him slumped over still attached to the VR equipment.

"Evacuate the gas immediately" ordered Graham.

"Evacuation complete, sir."

Casey jumped up and aimed his gun at the glass wall. "Walker, get ready!"

As Casey shot three times at the glass, Sarah crashed through the fragmented window and ran to Chuck, who was frighteningly still.

"Chuck, Chuck, you're gonna be alright. I've got you."

The last thing Chuck said was "Sar….rah?" before his eyes closed.


	4. Chapter 4

Part IV: It's a wonderful life

* * *

Beckman and Graham walked down the long sterile corridor to Casey, who was leaning against the wall, looking disheveled and tired.

"Agent Casey, shouldn't you get some rest. I'm sure our patient isn't going anywhere. Besides, the doctors tell me there should be no further complications."

"Yes, ma'am. I just want to be here when he wakes up."

Inside the room with all the beeps and whistles, attached to a heart rate monitor and brain wave recorder was Chuck. By his bedside was of course Sarah, who had not left his side since he collapsed in the beta unit's room.

The medical team stationed at the facility was able to reach Chuck in time and start him on a course of antidotes in order to counteract the poison. But still, it was touch and go for a while but now he seemed out of dire straits.

Still, even after hearing the news of his well being, Sarah did not leave his side, but now even she couldn't keep her eyes open. She fell asleep sitting on a chair next to his bed with her hand on his chest.

Chuck opened his eyes to see himself in an unfamiliar location. Last thing he saw was Sarah over him, crying. He realized that he was saved and was amazed that they were able to bring him back. _But then again they did bring Bryce back from a fatal gunshot to the chest, I guess even this is possible_.

He leaned over and saw Sarah sleeping in the chair next to him. Without disturbing her, he got out of the bed and wrapped her in his blanket. Also, noticing the breeze behind him, he put on his robe and exited the room.

One of the few times he left the door side, Casey felt the urge for food and left for a quick bite to eat. Chuck wandered out of the room and walked into the waiting room next door to watch the news playing on the TV. _Whoa, three days passed? I wonder what Ellie must be thinking._

Sarah awoke and was startled at the sight of an empty bed. She quickly jumped up and ran out of the room. First she ran up the corridor and then back down.

Seeing her frantically pacing, Chuck finally said "Hey Sarah. Did you lose something?"

"Chuck! I thought you…you were…." She quickly embraced him and didn't think of letting go, "Don't scare me like that!"

Chuck had a puzzled look on his face as he felt the outpouring of emotion from Sarah. "What's with that look?"

Chuck looked down into her eyes and said "nothing. Just thought I was dreaming."

"And why would you think that?"

"Well, that quite the outburst of emotion there Sarah. Just surprised me a bit."

"Its your fault you know, all these changes you've started."

"So do you have an answer?" Chuck asked.

"I'm…scared. But yes, I trust you."

A smile broke out on Chuck's face and he told her "don't worry I'll protect you from the Morgan's residing in my world."

They both shared a laugh and both knew the implications of the short conversation they just had.

Now Sarah didn't release her bear hug on Chuck until Casey showed up with Graham and Beckman in tow.

"Hey Casey, can I call this even for the crown vic?"

Laughing, he replied "let's call it three-fourths covered. I still have good memories of that car."

"Darn. I guess to cover the last fourth I'll have to save a smaller country. Maybe Spain or Denmark."

Now turning to Graham and Beckman, Chuck asked "did everything turn out ok? No international crises or new wars popped up? I just didn't wake up into Armageddon, did I?"

Graham replied "no Chuck, thanks to you they were all averted. Thank you again for what you did."

Beckman added "Yes, thanks Chuck. And I'd like to apologize for giving the order to eliminate you."

"No problem, if I had a dollar for every time a government agency wanted to kill me, then I'd be…."

Interrupting Chuck, Beckman said "There's another matter about the intersect. Since you are the only viable intersect, you will be back to full operational status. For the time being you will be employed, secretly of course, as a special agent for the CIA. You will continue to work with your partners, Sarah Walker and John Casey, seeing how you all get along so well. Continue the good work, Special Agent Bartowski."

"Thank you, General."

Turning to Sarah and Casey, "well guys it seems the old gang is back together."

Sarah, acting a bit shy, said "actually Chuck there is something we need to go over, it's about our cover. Beckman and Graham actually think there's a need for more increased security for the intersect. Our cover is being modified, from boyfriend and girlfriend to live-in couple."

"What?"


End file.
